Background: The objective of this paper is to quantify the cost of periodontitis management at public sector specialist periodontal clinic settings and analyse the distribution of cost components. Methods: Five specialist periodontal clinics in the Ministry of Health represented the public sector in providing clinical and cost data for this study. Newly-diagnosed periodontitis patients (N = 165) were recruited and followed up for one year of specialist periodontal care. Direct and indirect costs from the societal viewpoint were included in the cost analysis. They were measured in 2012 Ringgit Malaysia (MYR) and estimated from the societal perspective using activity-based and step-down costing methods, and substantiated by clinical pathways. Cost of dental equipment, consumables and labour (average treatment time) for each procedure was measured using activity-based costing method. Meanwhile, unit cost calculations for clinic administration, utilities and maintenance used step-down approach. Patient expenditures and absence from work were recorded via diary entries. The conversion from MYR to Euro was based on the 2012 rate (1€ = MYR4). Results: A total of 2900 procedures were provided, with an average cost of MYR 2820 (€705) per patient for the study year, and MYR 376 (€94) per outpatient visit. Out of this, 90% was contributed by provider cost and 10% by patient cost; 94% for direct cost and 4% for lost productivity. Treatment of aggressive periodontitis was significantly higher than for chronic periodontitis (t-test, P = 0.003). Higher costs were expended as disease severity increased (ANOVA, P = 0.022) and for patients requiring surgeries (ANOVA, P < 0.001). Providers generally spent most on consumables while patients spent most on transportation. Conclusions: Cost of providing dental treatment for periodontitis patients at public sector specialist settings were substantial and comparable with some non-communicable diseases. These findings provide basis for identifying potential cost-reducing strategies, estimating economic burden of periodontitis management and performing economic evaluation of the specialist periodontal programme.